PLOS Currents: Evidence on Genomic Tests

● Peer-Reviewed by distinguished researchers ● Open Access and freely available to all ● Open Data Compliant ● Archived in PubMed Central ● Indexed in PubMed & Scopus ● No Publication Fee

About PLOS Currents: Evidence on Genomic Tests

Genetic tests and other health-related applications of genomic research are increasingly available but information on their validity and utility is often fragmented and difficult to access. PLOS Currents: Evidence on Genomic Tests aims to provide summaries of available data and to highlight important gaps in knowledge.

PLOS Currents Goals

PLOS Currents is a publication channel that aims to address four facets of scholarly research communications: 1) Decrease publishing time with a streamlined review and production process. 2) Focus: Publish research within a focused research community. 3) Flexibility: Unlock rigid article formats to reflect diversity and broaden forms of research disseminated. 4) Revisions: Free the static research article with revisions that document research in progress.

Colorectal cancer is the third most common cancer and the second leading cause of cancer-related deaths in the United States. Screening has been shown to be effective in reducing colorectal cancer incidence and mortality. Colonoscopy, sigmoidoscopy, and fecal occult blood tests are all recommended screening tests that have widespread availability. Nevertheless, many people do not receive the evidence-based recommended screening for colorectal cancer. Additional stool-based methods have been developed that offer more options for colorectal cancer screening, including a variety of fecal DNA tests. The only fecal DNA test that is currently available commercially in the United States is ColoSure(TM), which is marketed as a non-invasive test that detects an epigenetic marker (methylated vimentin) associated with colorectal cancer and pre-cancerous adenomas. We examined the published literature on the analytic validity, clinical validity, and clinical utility of ColoSure and we briefly summarized the current colorectal cancer screening guidelines regarding fecal DNA testing. We also addressed the public health implications of the test and contextual issues surrounding the integration of fecal DNA testing into current colorectal cancer screening strategies. The primary goal was to provide a basic overview of ColoSure and identify gaps in knowledge and evidence that affect the recommendation and adoption of the test in colorectal cancer screening strategies.

Type 2 diabetes (T2D) is a common disease caused by a complex interplay between many genetic and environmental factors. Candidate gene studies and recent collaborative genome-wide association efforts revealed at least 38 common single nucleotide polymorphisms (SNPs) associated with increased risk of T2D. Genetic testing of multiple SNPs is considered a potentially useful tool for early detection of individuals at high diabetes risk leading to improved targeting of preventive interventions.

Hepatitis C virus (HCV) is a bloodborne infection that is one of the leading causes of liver disease. If left untreated, HCV can lead to cirrhosis, hepatocellular carcinoma, and death. The current standard of care for HCV is a combination of pegylated-interferon (peg-IFN) and ribavirin (RBV) in which the goal of treatment is to decrease complications and death due to HCV. HCV displays genetic polymorphism, where patients with HCV genotype 1 may have higher viral replication rates and are less likely to respond to treatment. These patients require a longer duration of treatment and a higher RBV dose. The interleukin (IL) 28B genotype test is associated with a sustained virologic response (SVR), defined as an undetectable HCV ribonucleic acid (RNA) upon completion of treatment and 24 weeks thereafter.

Tyrosine kinase inhibitors (TKIs) have revolutionized the treatment of chronic myeloid leukemia (CML). Although randomized evidence demonstrates that imatinib (a commercially available TKI) prolongs event-free survival in patients with CML, some patients develop imatinib intolerance or resistance. In addition, imatinib is less effective in patients who have progressed to more advanced disease stages, such as accelerated phase and blastic phase CML. For these reasons, 2nd generation TKIs that can inhibit the BCR-ABL protein more effectively or target additional disease mechanisms have been developed. Two such drugs have also been approved for clinical use by the FDA, nilotinib and dasatinib. Resistance to TKI treatment is thought to be mediated through various mechanisms, the most common of which is BCR-ABL1 mutations. Testing for mutations in BCR-ABL1 may predict lack of response to imatinib or may inform the choice between alternative TKIs.

Abacavir is a nucleoside reverse transcriptase inhibitor used for combination antiretroviral therapy for treating human immunodeficiency virus (HIV) infection. An adverse effect from abacavir is a treatment-limiting hypersensitivity reaction, which can be severe and potentially life-threatening. Abacavir-induced hypersensitivity reaction has been associated with the presence of the major histocompatibility complex class I allele HLA-B*5701. A screening test for the HLA-B*5701 allele can assist clinicians to identify patients who are at risk of developing a hypersensitivity reaction to abacavir.

Worldwide, lung cancer accounts for approximately 1 million deaths each year, making it the most common cause of cancer-related mortality. Non-small cell lung cancer (NSCLC) accounts for approximately 85% of lung cancer cases and is often associated with a relatively poor prognosis. The majority of NSCLC patients present with advanced disease and have an average 5-year survival rate of 5%. Currently, the standard of care for NSCLC includes treatment with a platinum-based chemotherapy regimen. However, not all patients benefit equally from such treatment. Therefore, recent pharmacogenomic studies have been performed in order to identify specific biomarkers that may allow for patient-tailored treatment strategies. One such biomarker is expression of the excision repair cross-complementation group 1 protein, ERCC1.

Coronary artery disease (CAD) is a leading cause of death worldwide and in the United States it is responsible for more than 500,000 deaths each year. Genome-wide association studies (GWAS) have revealed connections between a number of common single nucleotide polymorphisms (SNPs) and CAD and other cardiovascular diseases. The p.Trp719Arg SNP in the kinesin-like family 6 (KIF6) gene has recently been reported as a potential risk factor for CAD as well as a predictor of response to statin therapy.

Colon and rectal cancer (CRC) are the third most common cancer in the United States and cause approximately 50,000 deaths per year. The anti-epidermal growth factor receptor (EGFR) monoclonal antibodies cetuximab (Erbitux®) and panitumumab (Vectibix®) have been recently introduced to treat CRC. However, the response rate with these agents is low and they are associated with serious adverse effects. Accordingly biomarkers that can predict those patients that will respond to treatment may have clinical utility. The p.Val600Glu sequence variant (often called V600E) in the BRAF gene has been investigated as a biomarker to predict patients that will not respond to treatment with the anti-EGFR monoclonal antibodies.

It is estimated that approximately 22,000 Americans will be diagnosed with tumor of the brain or nervous system in 2010. Among primary brain tumors, approximately 60% are gliomas, the most common and most malignant of which is glioblastoma multiforme (GBM).The DecisionDx-GBM test is a multigene expression assay that is designed to predict which patients are likely to experience long-term (> 2 years) progression-free survival.

Tamoxifen, a selective estrogen receptor modulator, is the standard of care for premenopausal women with estrogen or progesterone receptor-positive breast cancer and a valid option for treating post-menopausal women. However, a substantial number of tamoxifen-treated patients relapse following surgical resection, while others remain disease-free for many years. It appears that the primary effectors of tamoxifen activity are its active metabolites, rather than tamoxifen itself. Cytochrome P450 (CYP) enzymes, CYP2D6 in particular, play a major role in the metabolism of tamoxifen to active metabolites. More than 75 germline CYP2D6 variants have been identified.

A test predicting lack of response to tamoxifen could supplement information used by clinicians and patients in treatment decision-making. For example, physicians and patients may opt to switch to an alternative therapy upfront.